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We've been approached to build an online store for a company that was previously an eBay shop.
Although, I've built shopping carts(from scratch) before using PayPal, this is the first where I'll be getting in software, Avactis, to do the hard stuff for me.

We just wanted a bit of advice first, before getting in too deep

I don't foresee any major issues in launching it. XHTML/CSS-ify the template, work it around the cart engine, speak to the bank, set up a payment gateway.